AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00780_tpal_reg_100.orf -o00780_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.53
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	TP0997	33	protease IV (sppA)
#2	TP0998	71	sodium/proton-dependent alanine transporter

Motif number 1

CACACATGAGGTGGAGGTTACA        	1	22	1	GTGGAGGTTA	     0.99544	-12
CAGATTAACTGTTCAGGACAATGC      	2	5	0	GTTCAGGACA	     0.98854	-67
CCTGCAGGGCGTGCAAGCTAACAGATTAAC	2	26	0	GTGCAAGCTA	     0.99732	-46
CTTGCACGCCCTGCAGGCTACCGACCCCGA	2	39	1	CTGCAGGCTA	    0.998126	-33
          **********

Masking position 5
Map Score:   6.23692

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 114
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

  TGTAACCTCCACCTCATGTGTGTTATGC	1	16	0	CCACCTCATG	    0.994138	-18
         GCATTGTCCTGAACAGTTAAT	2	2	1	CATTGTCCTG	    0.976175	-70
CTGTTAGCTTGCACGCCCTGCAGGCTACCG	2	32	1	GCACGCCCTG	    0.997476	-40
       TCGGCTCCTTCTGTCGGGGTCGG	2	59	0	GCTCCTTCTG	    0.994158	-13
          **********

Masking position 9
Map Score:   2.98785

Number of sites scoring better than the average of aligned sites = 621
Number in coding regions = 569
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

          **********

No masking
Map Score:   8.76972e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 4

          **********

No masking
Map Score:   8.76972e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   8.76972e-14

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0